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- EMDB-8244: Rigor myosin X co-complexed with an actin filament -

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Basic information

Entry
Database: EMDB / ID: EMD-8244
TitleRigor myosin X co-complexed with an actin filament
Map dataRigor myosin X co-complexed with an actin filament
Sample
  • Organelle or cellular component: Actin filament decorated by the myosin X motor domain
    • Protein or peptide: Unconventional myosin-X
    • Protein or peptide: Actin, alpha skeletal muscle
Keywordsmyosin molecular motors cytoskeletal motility / MOTOR PROTEIN
Function / homology
Function and homology information


plus-end directed microfilament motor activity / Netrin-1 signaling / positive regulation of cell-cell adhesion / filopodium tip / cytoskeleton-dependent intracellular transport / regulation of filopodium assembly / filopodium membrane / myosin complex / cytoskeletal motor activator activity / microfilament motor activity ...plus-end directed microfilament motor activity / Netrin-1 signaling / positive regulation of cell-cell adhesion / filopodium tip / cytoskeleton-dependent intracellular transport / regulation of filopodium assembly / filopodium membrane / myosin complex / cytoskeletal motor activator activity / microfilament motor activity / spectrin binding / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / actin filament bundle / filamentous actin / phosphatidylinositol-3,4,5-trisphosphate binding / actin filament bundle assembly / skeletal muscle thin filament assembly / striated muscle thin filament / skeletal muscle myofibril / actin monomer binding / skeletal muscle fiber development / stress fiber / titin binding / ruffle / actin filament polymerization / filopodium / actin filament / FCGR3A-mediated phagocytosis / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Regulation of actin dynamics for phagocytic cup formation / calcium-dependent protein binding / actin filament binding / lamellipodium / cell body / cell cortex / regulation of cell shape / calmodulin binding / hydrolase activity / neuron projection / protein domain specific binding / neuronal cell body / calcium ion binding / positive regulation of gene expression / nucleolus / magnesium ion binding / signal transduction / ATP binding / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Unconventional myosin-X, coiled coil domain / Class X myosin, motor domain / Myosin X, N-terminal SH3 domain / Myosin X, FERM domain C-lobe / Unconventional myosin-X coiled coil domain / Myosin X N-terminal SH3 domain / MyTH4 domain / MyTH4 domain superfamily / MyTH4 domain / MyTH4 domain profile. ...Unconventional myosin-X, coiled coil domain / Class X myosin, motor domain / Myosin X, N-terminal SH3 domain / Myosin X, FERM domain C-lobe / Unconventional myosin-X coiled coil domain / Myosin X N-terminal SH3 domain / MyTH4 domain / MyTH4 domain superfamily / MyTH4 domain / MyTH4 domain profile. / Domain in Myosin and Kinesin Tails / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain / IQ calmodulin-binding motif / FERM central domain / FERM/acyl-CoA-binding protein superfamily / Short calmodulin-binding motif containing conserved Ile and Gln residues. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / IQ motif, EF-hand binding site / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Actins signature 1. / Actin, conserved site / Actins signature 2. / Kinesin motor domain superfamily / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / ATPase, nucleotide binding domain / PH-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Actin, alpha skeletal muscle / Unconventional myosin-X
Similarity search - Component
Biological speciesHomo sapiens (human) / Oryctolagus cuniculus (rabbit)
Methodhelical reconstruction / cryo EM / Resolution: 9.1 Å
AuthorsSindelar CV / Houdusse A
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM 110530-01 United States
CitationJournal: Nat Commun / Year: 2016
Title: The myosin X motor is optimized for movement on actin bundles.
Authors: Virginie Ropars / Zhaohui Yang / Tatiana Isabet / Florian Blanc / Kaifeng Zhou / Tianming Lin / Xiaoyan Liu / Pascale Hissier / Frédéric Samazan / Béatrice Amigues / Eric D Yang / Hyokeun ...Authors: Virginie Ropars / Zhaohui Yang / Tatiana Isabet / Florian Blanc / Kaifeng Zhou / Tianming Lin / Xiaoyan Liu / Pascale Hissier / Frédéric Samazan / Béatrice Amigues / Eric D Yang / Hyokeun Park / Olena Pylypenko / Marco Cecchini / Charles V Sindelar / H Lee Sweeney / Anne Houdusse /
Abstract: Myosin X has features not found in other myosins. Its structure must underlie its unique ability to generate filopodia, which are essential for neuritogenesis, wound healing, cancer metastasis and ...Myosin X has features not found in other myosins. Its structure must underlie its unique ability to generate filopodia, which are essential for neuritogenesis, wound healing, cancer metastasis and some pathogenic infections. By determining high-resolution structures of key components of this motor, and characterizing the in vitro behaviour of the native dimer, we identify the features that explain the myosin X dimer behaviour. Single-molecule studies demonstrate that a native myosin X dimer moves on actin bundles with higher velocities and takes larger steps than on single actin filaments. The largest steps on actin bundles are larger than previously reported for artificially dimerized myosin X constructs or any other myosin. Our model and kinetic data explain why these large steps and high velocities can only occur on bundled filaments. Thus, myosin X functions as an antiparallel dimer in cells with a unique geometry optimized for movement on actin bundles.
History
DepositionJun 12, 2016-
Header (metadata) releaseSep 7, 2016-
Map releaseSep 7, 2016-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5kg8
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5kg8
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8244.png

Downloads & links

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Map

FileDownload / File: emd_8244.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRigor myosin X co-complexed with an actin filament
Voxel sizeX=Y=Z: 1.868 Å
Density
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.029098399 - 0.114953816
Average (Standard dev.)0.006837083 (±0.017238846)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-65-65-74
Dimensions128128128
Spacing128128128
CellA=B=C: 239.104 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.8681.8681.868
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z239.104239.104239.104
α/β/γ90.00090.00090.000
start NX/NY/NZ-152-37
NX/NY/NZ998271
MAP C/R/S123
start NC/NR/NS-65-65-74
NC/NR/NS128128128
D min/max/mean-0.0290.1150.007

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Supplemental data

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Mask #1

Fileemd_8244_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Rigor myosin X co-complexed with an actin filament, half map #1

Fileemd_8244_half_map_1.map
AnnotationRigor myosin X co-complexed with an actin filament, half map #1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Rigor myosin X co-complexed with an actin filament, half map #2

Fileemd_8244_half_map_2.map
AnnotationRigor myosin X co-complexed with an actin filament, half map #2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Actin filament decorated by the myosin X motor domain

EntireName: Actin filament decorated by the myosin X motor domain
Components
  • Organelle or cellular component: Actin filament decorated by the myosin X motor domain
    • Protein or peptide: Unconventional myosin-X
    • Protein or peptide: Actin, alpha skeletal muscle

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Supramolecule #1: Actin filament decorated by the myosin X motor domain

SupramoleculeName: Actin filament decorated by the myosin X motor domain / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all

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Macromolecule #1: Unconventional myosin-X

MacromoleculeName: Unconventional myosin-X / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 85.083086 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: NFFTEGTRVW LRENGQHFPS TVNSCAEGIV VFRTDYGQVF TYKQSTITHQ KVTAMHPTNE EGVDDMASLT ELHGGSIMYN LFQRYKRNQ IYTYIGSILA SVNPYQPIAG LYEPATMEQY SRRHLGELPP HIFAIANECY RCLWKRHDNQ CILISGESGA G KTESTKLI ...String:
NFFTEGTRVW LRENGQHFPS TVNSCAEGIV VFRTDYGQVF TYKQSTITHQ KVTAMHPTNE EGVDDMASLT ELHGGSIMYN LFQRYKRNQ IYTYIGSILA SVNPYQPIAG LYEPATMEQY SRRHLGELPP HIFAIANECY RCLWKRHDNQ CILISGESGA G KTESTKLI LKFLSVISQQ SLELSLKEKT SCVERAILES SPIMEAFGNA KTVYNNNSSR FGKFVQLNIC QKGNIQGGRI VD YLLEKNR VVRQNPGERN YHIFYALLAG LEHEEREEFY LSTPENYHYL NQSGCVEDKT ISDQESFREV ITAMDVMQFS KEE VREVSR LLAGILHLGN IEFITAGGAQ VSFKTALGRS AELLGLDPTQ LTDALTQRSM FLRGEEILTP LNVQQAVDSR DSLA MALYA CCFEWVIKKI NSRIKGNEDF KSIGILDIFG FENFEVNHFE QFNINYANEK LQEYFNKHIF SLEQLEYSRE GLVWE DIDW IDNGECLDLI EKKLGLLALI NEESHFPQAT DSTLLEKLHS QHANNHFYVK PRVAVNNFGV KHYAGEVQYD VRGILE KNR DTFRDDLLNL LRESRFDFIY DLFEHVSSRN NQDAAAAAAA ARRPTVSSQF KDSLHSLMAT LSSSNPFFVR CIKPNMQ KM PDQFDQAVVL NQLRYSGMLE TVRIRKAGYA VRRPFQDFYK RYKVLMRNLA LPEDVRGKCT SLLQLYDASN SEWQLGKT K VFLRESLEQK LEKRREEE

UniProtKB: Unconventional myosin-X

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Macromolecule #2: Actin, alpha skeletal muscle

MacromoleculeName: Actin, alpha skeletal muscle / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 41.827609 KDa
SequenceString: DEDETTALVC DNGSGLVKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IECGIITNWD DMEKIWHHT FYNELRVAPE EHPTLLTEAP LNPKANREKM TQIMFETFNV PAMYVAIQAV LSLYASGRTT GIVLDSGDGV T HNVPIYEG ...String:
DEDETTALVC DNGSGLVKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IECGIITNWD DMEKIWHHT FYNELRVAPE EHPTLLTEAP LNPKANREKM TQIMFETFNV PAMYVAIQAV LSLYASGRTT GIVLDSGDGV T HNVPIYEG YALPHAIMRL DLAGRDLTDY LMKILTERGY SFVTTAEREI VRDIKEKLCY VALDFENEMA TAASSSSLEK SY ELPDGQV ITIGNERFRC PETLFQPSFI GMESAGIHET TYNSIMKCDI DIRKDLYANN VMSGGTTMYP GIADRMQKEI TAL APSTMK IKIIAPPERK YSVWIGGSIL ASLSTFQQMW ITKQEYDEAG PSIVHRKCF

UniProtKB: Actin, alpha skeletal muscle

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration1.7 mg/mL
BufferpH: 6.8 / Component - Concentration: 5.0 mM / Component - Name: MOPS
GridModel: Quantifoil / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus max: 5.251 µm / Calibrated defocus min: 1.438 µm / Calibrated magnification: 26780 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 2 / Number real images: 154 / Average exposure time: 13.0 sec. / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
In silico model: 40 Angstrom low-pass filtered model of actomyosin
Final angle assignmentType: NOT APPLICABLE / Software - Name: FREALIGN (ver. 8.06)
Final reconstructionNumber classes used: 1
Applied symmetry - Helical parameters - Δz: 27.44 Å
Applied symmetry - Helical parameters - Δ&Phi: 167.1 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 9.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: FREALIGN (ver. 8.06)
Details: Symmetry was not applied in this reconstruction. The provided symmetry parameters are nominal, and were not actually used.
Number images used: 57927
FSC plot (resolution estimation)

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